HEADER MEMBRANE PROTEIN 28-APR-11 2YHC TITLE STRUCTURE OF BAMD FROM E. COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: UPF0169 LIPOPROTEIN YFIO; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 29-245; COMPND 5 SYNONYM: BAMD; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 469008; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET24D KEYWDS LIPOPROTEIN, ESSENTIAL BAM COMPONENT, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.ZETH,R.ALBRECHT REVDAT 2 10-AUG-11 2YHC 1 JRNL REMARK VERSN REVDAT 1 01-JUN-11 2YHC 0 JRNL AUTH R.ALBRECHT,K.ZETH JRNL TITL STRUCTURAL BASIS OF OUTER MEMBRANE PROTEIN JRNL TITL 2 BIOGENESIS IN BACTERIA. JRNL REF J.BIOL.CHEM. V. 286 27792 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21586578 JRNL DOI 10.1074/JBC.M111.238931 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0071 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 100.00 REMARK 3 NUMBER OF REFLECTIONS : 16896 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.20007 REMARK 3 R VALUE (WORKING SET) : 0.19831 REMARK 3 FREE R VALUE : 0.23262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 890 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.800 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.847 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1234 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.273 REMARK 3 BIN FREE R VALUE SET COUNT : 65 REMARK 3 BIN FREE R VALUE : 0.371 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1725 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.667 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.53 REMARK 3 B22 (A**2) : -0.44 REMARK 3 B33 (A**2) : 0.33 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.58 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.157 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.139 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.100 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.041 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1774 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2415 ; 2.095 ; 1.936 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 215 ; 5.794 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 99 ;38.216 ;24.040 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 289 ;19.081 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;16.730 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 255 ; 0.156 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1405 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1063 ; 1.320 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1710 ; 2.317 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 711 ; 4.005 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 701 ; 6.231 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 11 A 40 REMARK 3 ORIGIN FOR THE GROUP (A): 28.7807 31.1916 6.2709 REMARK 3 T TENSOR REMARK 3 T11: 0.2014 T22: 0.0290 REMARK 3 T33: 0.0906 T12: -0.0399 REMARK 3 T13: 0.0180 T23: 0.0270 REMARK 3 L TENSOR REMARK 3 L11: 4.9656 L22: 2.8769 REMARK 3 L33: 2.7929 L12: 0.6217 REMARK 3 L13: -0.1348 L23: -0.3655 REMARK 3 S TENSOR REMARK 3 S11: 0.0472 S12: 0.2085 S13: 0.4499 REMARK 3 S21: 0.0855 S22: -0.0983 S23: -0.0359 REMARK 3 S31: -0.3602 S32: 0.2007 S33: 0.0511 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 41 A 62 REMARK 3 ORIGIN FOR THE GROUP (A): 30.1939 23.0100 10.1827 REMARK 3 T TENSOR REMARK 3 T11: 0.0781 T22: 0.0133 REMARK 3 T33: 0.0513 T12: -0.0275 REMARK 3 T13: 0.0032 T23: -0.0019 REMARK 3 L TENSOR REMARK 3 L11: 3.7045 L22: 1.5557 REMARK 3 L33: 1.4309 L12: 0.5802 REMARK 3 L13: 0.2684 L23: 0.2619 REMARK 3 S TENSOR REMARK 3 S11: 0.0324 S12: -0.0461 S13: -0.0120 REMARK 3 S21: 0.0721 S22: -0.0173 S23: -0.1105 REMARK 3 S31: -0.1893 S32: 0.1161 S33: -0.0152 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 63 A 84 REMARK 3 ORIGIN FOR THE GROUP (A): 26.7608 14.2795 11.5769 REMARK 3 T TENSOR REMARK 3 T11: 0.0631 T22: 0.0056 REMARK 3 T33: 0.0845 T12: -0.0074 REMARK 3 T13: 0.0068 T23: 0.0121 REMARK 3 L TENSOR REMARK 3 L11: 3.8546 L22: 1.1959 REMARK 3 L33: 3.1862 L12: 0.2014 REMARK 3 L13: 1.2340 L23: 0.4032 REMARK 3 S TENSOR REMARK 3 S11: 0.1114 S12: -0.1036 S13: -0.3696 REMARK 3 S21: 0.0263 S22: -0.0077 S23: -0.1107 REMARK 3 S31: 0.1565 S32: 0.0310 S33: -0.1037 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 85 A 140 REMARK 3 ORIGIN FOR THE GROUP (A): 15.7440 12.0643 16.9061 REMARK 3 T TENSOR REMARK 3 T11: 0.0665 T22: 0.1045 REMARK 3 T33: 0.0987 T12: -0.0241 REMARK 3 T13: 0.0352 T23: 0.0424 REMARK 3 L TENSOR REMARK 3 L11: 7.5401 L22: 3.0223 REMARK 3 L33: 3.6888 L12: 3.6334 REMARK 3 L13: 0.7361 L23: 0.3104 REMARK 3 S TENSOR REMARK 3 S11: 0.0437 S12: -0.6024 S13: -0.5293 REMARK 3 S21: -0.0239 S22: -0.1352 S23: -0.2152 REMARK 3 S31: 0.1388 S32: -0.1412 S33: 0.0915 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 141 A 184 REMARK 3 ORIGIN FOR THE GROUP (A): 1.6043 -0.9952 14.6290 REMARK 3 T TENSOR REMARK 3 T11: 0.0424 T22: 0.1627 REMARK 3 T33: 0.0946 T12: -0.0534 REMARK 3 T13: 0.0300 T23: -0.0233 REMARK 3 L TENSOR REMARK 3 L11: 2.9072 L22: 5.2930 REMARK 3 L33: 0.6654 L12: 3.6010 REMARK 3 L13: 0.8582 L23: 0.9480 REMARK 3 S TENSOR REMARK 3 S11: -0.1410 S12: 0.0776 S13: 0.0458 REMARK 3 S21: -0.2747 S22: 0.1502 S23: 0.0220 REMARK 3 S31: -0.0948 S32: 0.0610 S33: -0.0092 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 185 A 233 REMARK 3 ORIGIN FOR THE GROUP (A): -2.0928 -3.4566 25.8886 REMARK 3 T TENSOR REMARK 3 T11: 0.0762 T22: 0.2031 REMARK 3 T33: 0.1274 T12: -0.0383 REMARK 3 T13: 0.0214 T23: -0.0130 REMARK 3 L TENSOR REMARK 3 L11: 1.7010 L22: 1.8520 REMARK 3 L33: 2.4916 L12: 1.4079 REMARK 3 L13: 1.6358 L23: 1.4326 REMARK 3 S TENSOR REMARK 3 S11: 0.0688 S12: -0.2454 S13: 0.0664 REMARK 3 S21: 0.2088 S22: -0.1162 S23: -0.0066 REMARK 3 S31: -0.0401 S32: -0.2235 S33: 0.0475 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2YHC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-APR-11. REMARK 100 THE PDBE ID CODE IS EBI-48152. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16896 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.80 REMARK 200 RESOLUTION RANGE LOW (A) : 40.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.9 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.2 REMARK 200 R MERGE (I) : 0.04 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.30 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.51 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.90 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: SHARP, DM, BUCCANEER REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 10% I-PROH, 0.1 REMARK 280 M HEPES PH 7.5 . REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 16.71400 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASP A 9 REMARK 465 ASN A 10 REMARK 465 SER A 102 REMARK 465 ALA A 103 REMARK 465 LEU A 104 REMARK 465 GLN A 105 REMARK 465 GLY A 106 REMARK 465 PHE A 107 REMARK 465 PHE A 108 REMARK 465 GLY A 109 REMARK 465 VAL A 110 REMARK 465 ASP A 111 REMARK 465 ARG A 112 REMARK 465 SER A 113 REMARK 465 ASP A 114 REMARK 465 ARG A 115 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU A 199 NH1 ARG A 203 1.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 147 CB - CG - CD1 ANGL. DEV. = 12.6 DEGREES REMARK 500 ARG A 203 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 140 -61.89 -29.13 REMARK 500 HIS A 228 24.60 -144.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 THR A 140 23.2 L L OUTSIDE RANGE REMARK 500 HIS A 232 24.0 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URE A1234 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YH9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DIMERIC BAME FROM E. COLI DBREF 2YHC A 9 225 UNP P0AC02 YFIO_ECOLI 29 245 SEQADV 2YHC LEU A 226 UNP P0AC02 EXPRESSION TAG SEQADV 2YHC GLU A 227 UNP P0AC02 EXPRESSION TAG SEQADV 2YHC HIS A 228 UNP P0AC02 EXPRESSION TAG SEQADV 2YHC HIS A 229 UNP P0AC02 EXPRESSION TAG SEQADV 2YHC HIS A 230 UNP P0AC02 EXPRESSION TAG SEQADV 2YHC HIS A 231 UNP P0AC02 EXPRESSION TAG SEQADV 2YHC HIS A 232 UNP P0AC02 EXPRESSION TAG SEQADV 2YHC HIS A 233 UNP P0AC02 EXPRESSION TAG SEQADV 2YHC GLN A 119 UNP P0AC02 HIS 139 CONFLICT SEQRES 1 A 225 ASP ASN PRO PRO ASN GLU ILE TYR ALA THR ALA GLN GLN SEQRES 2 A 225 LYS LEU GLN ASP GLY ASN TRP ARG GLN ALA ILE THR GLN SEQRES 3 A 225 LEU GLU ALA LEU ASP ASN ARG TYR PRO PHE GLY PRO TYR SEQRES 4 A 225 SER GLN GLN VAL GLN LEU ASP LEU ILE TYR ALA TYR TYR SEQRES 5 A 225 LYS ASN ALA ASP LEU PRO LEU ALA GLN ALA ALA ILE ASP SEQRES 6 A 225 ARG PHE ILE ARG LEU ASN PRO THR HIS PRO ASN ILE ASP SEQRES 7 A 225 TYR VAL MET TYR MET ARG GLY LEU THR ASN MET ALA LEU SEQRES 8 A 225 ASP ASP SER ALA LEU GLN GLY PHE PHE GLY VAL ASP ARG SEQRES 9 A 225 SER ASP ARG ASP PRO GLN GLN ALA ARG ALA ALA PHE SER SEQRES 10 A 225 ASP PHE SER LYS LEU VAL ARG GLY TYR PRO ASN SER GLN SEQRES 11 A 225 TYR THR THR ASP ALA THR LYS ARG LEU VAL PHE LEU LYS SEQRES 12 A 225 ASP ARG LEU ALA LYS TYR GLU TYR SER VAL ALA GLU TYR SEQRES 13 A 225 TYR THR GLU ARG GLY ALA TRP VAL ALA VAL VAL ASN ARG SEQRES 14 A 225 VAL GLU GLY MET LEU ARG ASP TYR PRO ASP THR GLN ALA SEQRES 15 A 225 THR ARG ASP ALA LEU PRO LEU MET GLU ASN ALA TYR ARG SEQRES 16 A 225 GLN MET GLN MET ASN ALA GLN ALA GLU LYS VAL ALA LYS SEQRES 17 A 225 ILE ILE ALA ALA ASN SER SER ASN THR LEU GLU HIS HIS SEQRES 18 A 225 HIS HIS HIS HIS HET URE A1234 4 HETNAM URE UREA FORMUL 2 URE C H4 N2 O FORMUL 3 HOH *84(H2 O) HELIX 1 1 PRO A 11 GLY A 26 1 16 HELIX 2 2 ASN A 27 TYR A 42 1 16 HELIX 3 3 TYR A 47 ASN A 62 1 16 HELIX 4 4 ASP A 64 ASN A 79 1 16 HELIX 5 5 ASN A 84 ASP A 101 1 18 HELIX 6 6 PRO A 117 ARG A 132 1 16 HELIX 7 7 TYR A 139 GLY A 169 1 31 HELIX 8 8 ALA A 170 TYR A 185 1 16 HELIX 9 9 THR A 188 MET A 205 1 18 HELIX 10 10 MET A 207 ASN A 221 1 15 SITE 1 AC1 4 ALA A 173 ASN A 176 ARG A 177 HOH A2065 CRYST1 53.112 33.428 57.783 90.00 111.41 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.018828 0.000000 0.007382 0.00000 SCALE2 0.000000 0.029915 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018589 0.00000